Flipons enable genomes to learn by intermediating the exchange of energy for information

Journal of The Royal Society Interface, Journal Year: 2025, Volume and Issue: 22(224)

Published: March 1, 2025

Recent findings have confirmed the long-held belief that alternative DNA conformations encoded by genetic elements called flipons important biological roles. Many of these structures are formed sequences originally spread throughout human genome endogenous retroelements (ERE) captured 50% territory before being disarmed. Only 2.6% remaining codes for proteins. Other organisms instead streamlined their genomes eliminating invasive and other repeat elements. The question arises, why retain any ERE at all? A new synthesis suggests enable to learn programme context-specific readout information altering transcripts produced. exchange energy is mediated through changes in topology. Here I provide a formulation how describe underlying p-bit algorithm which tuned. framework strategies therapeutic reprogramming cells.

Language: Английский

Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(9), P. 4032 - 4032

Published: April 24, 2025

Genomic sequences that form three-stranded triplexes (TPXs) under physiological conditions (called T-flipons) play an important role in defining DNA nucleosome-free regions (NFRs). Within these NFRs, other flipon types can cycle conformations to actuate gene expression. The transcripts read from the NFR condensates engage proteins and small RNAs. helicases bound then trigger RNA polymerase release by dissociating 7SK ribonucleoprotein. TPXs formed usually incorporate as third strand. made only arise mostly during replication. Many (sRNAs) long noncoding (lncRNA) direct TPX formation. with circular RNAs have greater stability specificity than those linear LncRNAs affect local expression through formation transcriptional interference. seeded lncRNAs are updated feedback loops involving genes they regulate. Some also target distant loci a sequence-specific manner. Overall, rapidly evolve adding or subtracting sequence motifs modify nucleate. show less conservation protein-coding sequences. sRNAs help place nucleosomes restrict endogenous retroelement (ERE) silencing of EREs starts early embryogenesis is essential for bootstrapping development. Once system set, different role, notable enrichment Short Interspersed Nuclear Repeats (SINEs) Enhancer–Promoter condensates. highly programmable TPX-dependent processes create chromaverse capable many complexities.

Language: Английский